Use these PATE functions to process the data from GCS

pate-rnd xmap-collector --include_file_str QC_Gamma \
--out_file_name gamma_qc.csv

Use this to import the data into JH from GCS

gsutil cp gs://inhouse-xmap-data/user_data_frames/gamma_qc.csv
/home/ddhillon/projects/beta-av-testing/data/raw/gamma_qc.csv

Introduction

This is a one off quick check experiment to make sure everything looks ok

benchling

## New names:
## * `` -> ...1

There are two runs for panel 2 - why? this is because one of the QCs for the march 3rd run was switched and Jinesh and Wilson changed the platemap and re-ran the software

We will only use the 7th march data since it has the correct positioning

## # A tibble: 3 × 2
##   file_name                                        n
##   <chr>                                        <int>
## 1 20220303_QC_Gamma_Panel1_20220304_135209.csv  4608
## 2 20220303_QC_Gamma_Panel2_20220304_133848.csv  3072
## 3 20220307_QC_Gamma_Panel2_20220307_141423.csv  3072

Analysis

Estimate Beta using Gamma Curve

We take the curve fit by gamma, and then interpolate the beta standards and check the concentrations. We will then use these interpolated concentrations to see what the % recovery is, and whether it is within the expected interval we expect it to be.

## New names:
## * `` -> ...1
## # A tibble: 42 × 3
##    xponent_id assay       n
##    <chr>      <chr>   <int>
##  1 Standard1  CEA       231
##  2 Standard1  FLT3L     261
##  3 Standard1  IL-1 R2   258
##  4 Standard1  IL-8      255
##  5 Standard1  MUC-16    259
##  6 Standard1  TNC       232
##  7 Standard1  WFDC2     231
##  8 Standard2  CEA       236
##  9 Standard2  FLT3L     262
## 10 Standard2  IL-1 R2   259
## # … with 32 more rows
## `summarise()` has grouped output by 'xponent_id'. You
## can override using the `.groups` argument.
## # A tibble: 42 × 3
##    xponent_id assay       n
##    <chr>      <chr>   <int>
##  1 Standard1  CEA         1
##  2 Standard1  FLT3L       1
##  3 Standard1  IL-1 R2     1
##  4 Standard1  IL-8        1
##  5 Standard1  MUC-16      1
##  6 Standard1  TNC         1
##  7 Standard1  WFDC2       1
##  8 Standard2  CEA         1
##  9 Standard2  FLT3L       1
## 10 Standard2  IL-1 R2     1
## # … with 32 more rows

Now we take the beta_interpolated data and merge it with our historical data

gsutil cp /home/ddhillon/projects/beta-av-testing/notebooks/gamma-lot-qc/outputs/exp-01.html gs://freenome-user-data-ddhillon/outputs/